This follows many of the basic skill challenge guidelines. The DCs and required successes are set exactly as the Skill Challenge rules are laid out. "Special Rules" take the place of "Advantages" but are the exact same thing with a different name. Since Units only have 6 "skills" with which to make checks, I eliminated the rule that allows for limited successes with any given skill; in fact, I codified that rule by outlining exactly which competencies were required, and in what amounts, to win the mission.

I build a challenge by outlining exactly what the mission is supposed to be. If it should be simple for the PCs to send minions to accomplish this, I make it PC level -2. If it should be a moderate challenge, I set it to PC level+1, and if it should be practically impossible, but within reach, I set it to PC level +4. Then, to set complexity, I make a list of things they will have to accomplish to win, i.e how many checks they will need to make. This helps me gain an understanding of how complex the mission needs to be.

In the above sample, I knew that, per The Forge of War, Cyre's elite adventuring/espionage group, the Champions of the Bell, gain fame for saving Duke Korlan, so I didn't want it to be easy for the Prince and his Order to Change history; it could be possible, but not easy, so the difficulty was set at level 8 (Level 4 PC + 4). Then I set the challenges. To win, the adventurers would need to:

Make an excuse to be at the northern border or get permission from the Queen to invade Karrnath. (Intrigue)

Get out of Cyre without the rest of the military noticing (Espionage)

Move past the Karrnathi border patrol without engaging the army (Espionage)

Find out where the Duke is being held Prisoner (Research, Observation, or Intrigue)

Get to the prison (Espionage or Combat)

Figure out a way inside the prison (Research, Observation, or Intrigue)

Break into the Prison (Espionage or Combat)

Get back out of Karrnath with the Duke (Espionage or Combat)

With 8 distinct tasks, it seemed complexity 3 was perfect. I selected 2 cases of moderate success with hitting easy DC for Espionage checks because the essence of this mission was espionage: I wanted whomever attempted this mission to feel like they could at least compete, even if Espionage wasn't their main deal.

Things I still need to consider about missions:

1. How should I handle missions when a PC wants to send multiple units on a mission together? My initial reaction was to use whichever unit had the best competency for each roll, but to assign failures to both sets of stamina, no matter who made the check. I would consider opening it up, allowing the PC to pick which of the multiple units would make each check, only penalizing the unit who attempting the task, and even allowing aid-another checks, with the drawback that a failure would penalize both units. I'd love to debate the virtues of both systems with anyone who has ideas, and would also appreciate any alternate ideas anyone might have.

2. Can a PC do a mission without being attached to another unit? I have a PC whose unit ALWAYS failed missions, because dice rolls were bad and their math was never quite good enough. The PC wanted to just do the missions solo, but if just the PC were doing the mission, why not just run it? Time constraints and the desire to entertain everyone nixed that idea, but after looking at what some LARPs are experimenting with, concerning how much can be done with in-between game actions, I decided to consider ways to let individual PCs (or small groups of them) attempt missions. Should I just let them make appropriate skill challenges instead of competencies? Should I convert them into "Heroic Unit" stats somehow and let them try the mission the same way an NPC would? Would that allow me to eliminate the attachment rules I am not happy with and just let the PC's "Mission Stats" also go on the mission?